Spatial motifs reveal patterns in cellular architecture of complex tissues
Zainalabedin Samadi, Amjad Askary
bioRxiv 2024.04.08.588586, 2024. online article, pdf.

Lineage motifs as developmental modules for control of cell type proportions
Martin Tran, Amjad Askary*, Michael Elowitz*
Developmental Cell 59 (6): 812–26.e3. online article, pdf.
* corresponding authors

osr1 couples intermediate mesoderm cell fate with temporal dynamics of vessel progenitor cell differentiation
Elliot Perens, Jessyka Diaz, Agathe Quesnel, Amjad Askary, Gage Crump, Deborah Yelon
Development 148(15), dev198408, 2021. online article, pdf.

In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription
Amjad Askary, Luis Sanchez-Guardado, James M Linton, Duncan M Chadly, Mark W Budde, Long Cai, Carlos Lois, Michael B Elowitz
Nature Biotechnology 38(1), 66-75, 2020. online article, pdf.

Genome-wide analysis of facial skeletal regionalization in zebrafish
Amjad Askary, Pengfei Xu, Lindsey Barske, Maxwell Bay, Paul Bump, Bartosz Balczerski, Michael A Bonaguidi, J Gage Crump
Development 144(16), 2994-3005, 2017. online article, pdf.

Building and maintaining joints by exquisite local control of cell fate
Joanna Smeeton, Amjad Askary, J Gage Crump
Wiley Interdisciplinary Reviews: Developmental Biology 6(1), e245, 2017. online article, pdf.

Ancient origin of lubricated joints in bony vertebrates
Amjad Askary, Joanna Smeeton, Sandeep Paul, Simone Schindler, Ingo Braasch, Nicholas A Ellis, John Postlethwait, Craig T Miller, J Gage Crump
eLife 5, e16415, 2016. online article, pdf.

Competition between Jagged-Notch and Endothelin1 signaling selectively restricts cartilage formation in the zebrafish upper face
Lindsey Barske, Amjad Askary, Elizabeth Zuniga, Bartosz Balczerski, Paul Bump, James T Nichols, J Gage Crump
PLoS Genetics 12(4), e1005967, 2016. online article, pdf.

Iroquois proteins promote skeletal joint formation by maintaining chondrocytes in an immature state
Amjad Askary, Lindsey Mork, Sandeep Paul, Xinjun He, Audrey K Izuhara, Suhasni Gopalakrishnan, Justin K Ichida, Andrew P McMahon, Sonja Dabizljevic, Rodney Dale, Francesca V Mariani, J Gage Crump
Developmental Cell 35(3), 358-365, 2015. online article, pdf.
Preview:  M.P. Harris, M.B. Hawkins. Developmental Cell

Modeling of the RAG reaction mechanism
Amjad Askary, Noriko Shimazaki, Niki Bayat, Michael R Lieber
Cell reports 7(2), 307-315, 2014. online article, pdf.

Mechanistic basis for RAG discrimination between recombination sites and the off-target sites of human lymphomas
Noriko Shimazaki, Amjad Askary, Patrick C Swanson, Michael R Lieber
Molecular and Cellular Biology 32(2), 365-375, 2012. online article, pdf.

N4: a precise and highly sensitive promoter predictor using neural network fed by nearest neighbors
Amjad Askary, Ali Masoudi-Nejad, Roozbeh Sharafi, Amir Mizbani, Sobhan Naderi Parizi, Malihe Purmasjedi
Genes & Genetic Systems 84(6), 425-430, 2009. online article, pdf.